Where is this company located? If it's Silicon Valley, those numbers are very low. If it's Idaho, that's a different story. So we need to know that, and more importantly, we need to know what salary you want (is the $100k and 0.22% what you really want, or what you thought they'd agree to?).

First of all, I hope you didn't tell them that $96k number before they offered $100k. If so, you screwed yourself by anchoring your offer to a low previous salary.

Second, if they are even discussing salary, it means they like you and they have already mentally committed to you. Going back to the drawing board will mean weeks or months of reading resumes, interviews, negotiations, and possibly recruiting fees which will cost easily $20-40k. In that light, giving you $20k extra would be a bargain. The fact that they went from $96k to $106k proves that.

Third, I wouldn't let equity be the deciding factor (that could just be me), since it could be worth $0 (and 90% of the time it probably is).

As far as negotiating, I suggest you read this post in full: http://www.kalzumeus.com/2012/01/23/salary-negotiation/